[galaxy-user] matlab + galaxy

Hi, How can I call Matlab command in Galaxy ? I refer this link, but don't know how to use it. https://wiki.galaxyproject.org/HelpOnParsers?action=fullsearchcontext=180value=mutsigfullsearch=Text I am learning Galaxy, hence don't know much about it. Can i write that command in xml file to

[galaxy-user] upload more than 2GB data from local computer to local installation of galaxy

Hi, I am unable to upload more than 3 GB data from local computer to local installation of galaxy. How can I do that ? I saw many of the tutorials which says about online upload. My Galaxy is running on 127.0.0.7:8080 I tried FileZilla to upload file, but its says Connection established, waiting

Re: [galaxy-user] upload more than 2GB data from local computer to local installation of galaxy

How can I create ftp for my local computer to upload data for local galaxy installation ? For current I may can use normal text upload but if I am having 10-20 GB file then I will need FTP upload. Waiting for positive reply. Hi, I am unable to upload more than 3 GB data from local computer to

[galaxy-user] large data to upload problem

Hi, Thank You for answers, I am able to learn everyday. I am having 500 GB hard disk, I am trying to integrate 'x' tool to galaxy for local lab purpose. 'x' tool require bam files which are of 400 GB file size. When I used Admin section to upload file my computer hang because of no space. Is it

Re: [galaxy-user] large data to upload problem

Hi, Thank You for reply. I am still not clear about this website. https://wiki.galaxyproject.org/Admin/Config/Upload%20via%20FTP There are total 4 main points highlighted in this website. Do I have to follow all 4 points ? I have tried just on second point which is Configuring Galaxy As I just

[galaxy-user] Galaxy + user program unable to locate files

Hi, Thank You for your kind reply. I am having problem in running command in Galaxy. my current command: tool_name file_having_multiple_file_name_tab_delimited.txt or .tab file1.bam file2.bam /usr/bin/x_tool fileList.tab file1.bam file2.bam I have created xml file so that i can

Re: [galaxy-user] Galaxy + user program unable to locate files

to* /home/user/Documents/* then run commands, hence all files listed in *fileList.tab* are accessible to software. On Thu, Feb 27, 2014 at 3:32 PM, Peter Cock p.j.a.c...@googlemail.comwrote: On Thu, Feb 27, 2014 at 9:32 AM, do kadya doka...@gmail.com wrote: Hi, Thank You for your kind reply

[galaxy-user] unable to find the file

Respected Sir / Ma'am, 'x' tool having 3 commands, 1) command takes files from path. ex perl x.pl --mode 1 file1.bam file2.bam file3.fasta --output result1.txt 2) file4 must have name of result1.txt, file1.bam, file2.bam perl x.pl --mode 2 file4.txt --output-directory ~/result2/ for this

[galaxy-user] upload data to galaxy using terminal

Hi, Can I upload data (mostly link the data) using terminal ? MuSiC 2 tool integration is not available in their website nor in tool shed. MuSiC 2 creates folder and files by itself, which is hard to track by Galaxy. So is there any way to link files to galaxy current work space so that I can

Re: [galaxy-user] upload data to galaxy using terminal

://galaxy-central.readthedocs.org/en/latest/lib/galaxy.webapps.galaxy.api.html#module-galaxy.webapps.galaxy.api.library_contents Martin On Tue, Mar 25, 2014 at 7:47 AM, do kadya doka...@gmail.com wrote: Hi, Can I upload data (mostly link the data) using terminal ? MuSiC 2 tool integration

[galaxy-user] error while running Intogen.

Respected Sir / Ma'am, I was running Intogen using galaxy, I changes parameters name and then this error came. Can you please tell what is the meaning of this error ? Traceback (most recent call last): File /home/ganit/galaxy_work/galaxy-dist/lib/galaxy/jobs/runners/__init__.py, line 123, in